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JAL-3633 ensure check both http:// or https:// for urls
author
Ben Soares
<b.soares@dundee.ac.uk>
Wed, 8 Jul 2020 16:01:32 +0000
(17:01 +0100)
committer
Ben Soares
<b.soares@dundee.ac.uk>
Thu, 12 Nov 2020 17:42:51 +0000
(17:42 +0000)
src/jalview/bin/Jalview.java
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src/jalview/gui/AlignFrame.java
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src/jalview/project/Jalview2XML.java
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src/jalview/util/HttpUtils.java
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diff --git
a/src/jalview/bin/Jalview.java
b/src/jalview/bin/Jalview.java
index
06f3a47
..
6a67750
100755
(executable)
--- a/
src/jalview/bin/Jalview.java
+++ b/
src/jalview/bin/Jalview.java
@@
-67,6
+67,7
@@
import jalview.io.NewickFile;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.jws2.Jws2Discoverer;
@@
-531,8
+532,7
@@
public class Jalview
* @j2sIgnore
*/
{
* @j2sIgnore
*/
{
- if (!file.startsWith("http://") && !file.startsWith("https://"))
- // BH 2019 added https check for Java
+ if (!HttpUtils.startsWithHttpOrHttps(file))
{
if (!(new File(file)).exists())
{
{
if (!(new File(file)).exists())
{
diff --git
a/src/jalview/gui/AlignFrame.java
b/src/jalview/gui/AlignFrame.java
index
4354ac6
..
e886ad0
100644
(file)
--- a/
src/jalview/gui/AlignFrame.java
+++ b/
src/jalview/gui/AlignFrame.java
@@
-144,6
+144,7
@@
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@
-1062,7
+1063,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
@@
-1078,9
+1079,9
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
if (fileObject == null)
{
if (fileObject == null)
{
- DataSourceType protocol = (fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
? DataSourceType.URL
- : DataSourceType.FILE);
+ : DataSourceType.FILE;
newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
currentFileFormat);
}
newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
currentFileFormat);
}
@@
-1131,7
+1132,7
@@
public class AlignFrame extends GAlignFrame implements DropTargetListener,
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed();
}
{
saveAs_actionPerformed();
}
diff --git
a/src/jalview/project/Jalview2XML.java
b/src/jalview/project/Jalview2XML.java
index
ccd9ab0
..
aa4cd6c
100644
(file)
--- a/
src/jalview/project/Jalview2XML.java
+++ b/
src/jalview/project/Jalview2XML.java
@@
-29,6
+29,8
@@
import java.awt.Font;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
import java.awt.Rectangle;
import java.io.BufferedReader;
import java.io.ByteArrayInputStream;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
@@
-107,6
+109,7
@@
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.AppVarna;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.AppVarna;
+import jalview.gui.ChimeraViewFrame;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
@@
-133,6
+136,7
@@
import jalview.schemes.UserColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.StringUtils;
@@
-957,7
+961,7
@@
public class Jalview2XML
else
{
vamsasSeq = createVamsasSequence(id, jds);
else
{
vamsasSeq = createVamsasSequence(id, jds);
-// vamsasSet.addSequence(vamsasSeq);
+ // vamsasSet.addSequence(vamsasSeq);
vamsasSet.getSequence().add(vamsasSeq);
vamsasSetIds.put(id, vamsasSeq);
seqRefIds.put(id, jds);
vamsasSet.getSequence().add(vamsasSeq);
vamsasSetIds.put(id, vamsasSeq);
seqRefIds.put(id, jds);
@@
-1401,7
+1405,7
@@
public class Jalview2XML
}
}
}
}
- //jms.setJGroup(groups);
+ // jms.setJGroup(groups);
Object group;
for (JGroup grp : groups)
{
Object group;
for (JGroup grp : groups)
{
@@
-2788,11
+2792,13
@@
public class Jalview2XML
viewportsAdded.clear();
frefedSequence = null;
viewportsAdded.clear();
frefedSequence = null;
- if (file.startsWith("http://")) {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider() {
+ if (HttpUtils.startsWithHttpOrHttps(file))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
+ {
@Override
public JarInputStream getJarInputStream() throws IOException {
@Override
public JarInputStream getJarInputStream() throws IOException {
diff --git
a/src/jalview/util/HttpUtils.java
b/src/jalview/util/HttpUtils.java
index
a5a9460
..
74f77a2
100644
(file)
--- a/
src/jalview/util/HttpUtils.java
+++ b/
src/jalview/util/HttpUtils.java
@@
-64,4
+64,9
@@
public class HttpUtils
return false;
}
return false;
}
+ public static boolean startsWithHttpOrHttps(String file)
+ {
+ return file.startsWith("http://") || file.startsWith("https://");
+ }
+
}
}